Full package name: mesquite.trees.ManageTrees.ManageTrees Duty: Manager of lists of trees, including read/write TREES block (mesquite.lib.duties.TreesManager)
Module Explanation
Manages tree blocks (including read/write TREES block in NEXUS file).
Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70
Commands of Manage TREES blocks
getTreeBlock
Explanation: Returns a trees block
Parameters: [number of trees block; 0 based]
showTrees
Explanation: Shows lists of trees in a trees block
Parameters: [number of trees block; 0 based]
showTreesInWindow
Explanation: Shows a tree window showing a particular trees block
Parameters: [number of tree block to show]
exportTreesBlock
Explanation: Saves copy of a trees block to a separate file
Parameters: [index of trees block]
exportTreesBlocks
Explanation: Saves copies of a series of tree blocks to files
Parameters: [name of module to fill the trees blocks]
showTreeBlocks
Explanation: Shows a list of the stored tree blocks
deleteTreeBlocks
Explanation: Deletes tree blocks from the project
restartTreeSource
Explanation: Restarts to unfinished tree block filling
Parameters: [name of tree block filler module]
reconnectTreeSource
Explanation: Reconnects to unfinished tree block filling
Parameters: [name of tree block filler module]
treesReady
Explanation: Informs Manage trees that trees are ready
Parameters: [ID of tree block filler module]
fireTreeSource
Explanation: Fires the tree source for use in filling newly created tree blocks
setTreeSource
Explanation: Sets the tree source for use in filling newly created tree blocks
Parameters: [name of tree block filler module]
linkTreeFile
Explanation: Links file with trees
includeTreeFile
Explanation: Includes file with trees
includePartialTreeFile
Explanation: Includes file with trees (partial)
setDefaultNumericalLabelInterpetation
Explanation: Sets the interpretation of numerical node labels, as per dialog in this module
Parameters: [true/false for interpret as numerical; true/false for as on branches; name of interpretation]
includeTreeFileAskPartial
Explanation: Includes file with trees (ask if partial)
newTreeBlock
Explanation: Creates a new tree block
Parameters: [reference of taxa block] [identification number of file to which tree block will belong] [name of tree block]
concatLastTwo
Explanation: Concatenates the last tree block into the second last
disposeLastTreeBlock
Explanation: Disposes the last block of trees
newFilledTreeBlockIntS
Explanation: Creates a new filled tree block (internally called, used for scripting)
Parameters: [reference of taxa block] [optional -- if id then next token is id not number][number of file in which the tree block should be stored] [name of tree block] [how many trees to make]
newFilledTreeBlockInt
Explanation: Creates a new filled tree block (internally called from menu item)
Parameters: [name of tree source module]
saveDrectTreeFileInt
Explanation: Creates a new tree file written directly from a tree source (internally called from menu item)
Parameters: [name of tree source module]
newFilledTreeBlockInferenceInt
Explanation: Creates a new filled tree block (internally called from menu item) using a tree inference procedure
